search for: limmagui

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seem...

Full_Name: Edoardo Giacopuzzi Version: 2.0.1 OS: Windows XP Home Submission from: (NULL) (80.181.65.157) I have some problem with this new version of R GUI. I've used limmaGUI package with an older version of R and it works perfectlly, but now with the last version R 2.0.1.0 two error boxs appear every time I try to launch this package: 1. <<Error in list.files(path, pattern, all.files, full.names, recursive): regular expressione 'pattern' not valid>>...

Hello, In limmaGUI, after running a linear model for a single gene & time point (mutant vs control), the venn-diagram for differentially expressed genes with a p-value cut-off gives a different number than the top-table with the same cut-off (2600 vs. 791). I have seen the same thing happen before for multiple t...

...d do... I am just wondering approximately how many people use / have used some of the R stuff I've developed (and in how many countries). In particular I'm talking about the R-Tcl/Tk examples I've put at http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/ and/or my two BioC packages limmaGUI and affylmGUI (now maintained by Keith Satterley), and/or the IBC2004 and JSM2005 microarray analysis course websites. If it's not too much trouble, could you please tell me [OFF THE LIST] if you use / have used any of these things (otherwise don't reply) and what country you are from, and...

...est that when checkS3methods() (called by R CMD check) fails because of a syntax error in a dependent package listed in the DESCRIPTION file of the main package being checked, it would be nice if checkS3methods() reported which dependent package caused it to fail? Running R CMD check on my package limmaGUI, revealed a syntax error in one of limmaGUI's dependent packages, which turned out to be the R2HTML package (after a bit of sleuthing). Here's the syntax error in R2HTML, caused by the new parsing rules for associative use of relational operators: x0 <- xm[okP] == 0 != (as.numeric(Cf...

Hi all, I'm working on microarray and currently analyzing the microrarray data using limmaGUI. Loop design has been applied in this experiment. This is a 2X2 factorial experiment where there are control and treatment at 2 different time points, week 6 and 9. The experimental design is almost the same as the limmaGUI work example: Weaver Data set. I would like to look at the effect of time,...

...iled for 'tcltk' I have done a couple of remedies: 1) Tried installing tcl and tk 8.4 from source 2) Tried to install the version of tcltk from the fink sourceforge net. 3) Tried to change the path and it does not work. Does anyone have a solution to this problem as I need tcltk to run limmaGUI? Best regards, Bernard

...ate if others can confirm similar behaviour. Can anyone suggest why it worked under R-2.13.x but not in later versions of R. Was there a change in R that impacts with this aspect of tcltk? Is there a work around for this problem? Any suggestions appreciated, thanks Keith Satterley affylmGUI, limmaGUI maintainer. Bioinformatics Division The Walter and Eliza Hall Institute Melbourne, Australia. Some sessionInfo() outputs: Win7-64bit-R-2.15.2 testGUI() fails intermittently. > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Engl...

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...============ -- Proteomics (PROcess, gpls, apComplex) -- Array CGH (DNAcopy, aCGH) -- Cell cycle analysis (GeneTS) -- Packages for lab assay analysis and management (prada) -- Agilent arrays handling in limma -- Annotation tools (Resourcer, GOstat, goTools, ontoTools) -- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -- affymetrix processing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packag...

Hello, Following a discussion initiated on r-devel, that mentions SciViews-R and other GUIs issues for R, I would like to make comments (and would be happy if these comments would initiate interesting initiatives). A big, big problem with SciViews-R is that a part of it is written in Visual Basic 6, a M$$$$ language, not supported any more, buggy, non transposable to other platforms, etc,